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R script for co-occurrence stats and figures
This R script performs statistical analyses and generates figures used in Ecology Letters paper American Journal of Botany paper "No association between plant mating system and... -
Tempelton's Tests files
This zipped folder contains all files used for the Templeton's test. This folder is organised in subfolders, whereas "1 - Pasimony Analysis Input files" contains the... -
Literature Sample2: 40 recently published phylogeny-related articles
We searched Thomson Reuters Web of Science (WoS) in May of 2011 for articles matching 'phylogen' in title or 'topic'. WoS sorted the results by 'relevance', and we picked 40... -
Stein et al. 2015 Fig. 1 in newick file format
Phylogenetic hypothesis resulting from analysis of the molecular data matrix in the newick file format. -
HawaiianTaro_SNP.fas
ZIP archive of two SNP datasets used for phylogenetic analyses in FASTA format, homozygous positions only (nomenclature see VCF files). -
Lepidoptera Bait Design and Testing Files
The ZIP archive contains the files used to identify, design, and test probes targeting conserved loci in Lepidoptera. The -design-steps.md file is a description of the design... -
Results of monoculture experiment
Measurements of OD and fluorescence intensity in the monoculture experiment for 12 bacterial strains. Column names represent: Raw data Number, Microplate Row, Microplate Column,... -
fossil_calibration_analyses(BEASTv2.2)
XML file for running the analyses with the Brassicaceae dataset (supermatrix approach) in BEASTv2.2 (Bouckaert et al., 2014) using the four Brassicales fossil scheme for... -
BAMM_files
Input and output files of BAMM analyses conducted under six different values for the prior on the expected number of diversification shifts (0.1, 1, 5, 10, 50, 100). (1) Control... -
mtDNA_simple
This is a nexus file that includes alignments of mitochondrial DNA sequences that were analyzed in this study -
Supplementary Archive 3
Supplementary Archive 3: This archive contains following subdirectories i) subdirectory supermatrix_209_loci and ii) subdirectory ML_inference (see README) -
Input file NDnl analysis
This is the XML file which configures all parameters for the BEAST program for the Bayesian MCMC analysis using the node dating approach with narrow prior calibration densities.... -
ReadMapping.LIB0249.B.ampliatum.DNA4245
A SAM file with the results of mapping shotgun sequencing reads (available on SRA) from Bembidion ampliatum (Maddison voucher DNA4245) to a reference sequence (included in this...
